ROCOCO reconstructs ancestral gene clusters. Given the topology of a phylogenetic tree
and the gene orders of the leaf nodes, it calculates optimal sets of gene clusters for
the inner nodes. The optimization criterion combines two properties: parsimony, i.e. the
number of gains and losses of gene clusters has to be minimal, and consistency, i.e. for
each ancestral node, there must exist at least one potential gene order that contains all
the reconstructed clusters.

The underlying model, the labelling problem and the method are introduced in [STO:WIT:2009] by
Stoye and Wittler. A more recent, extensive description can be found in [WIT:2010]

In the current version (2.0), two sequence-based gene cluster models are included. That means, paralogs in the gene order are incorporated in the model. ROCOCO
provides a graphical user interface (ROCOCO-Compare) to compare and explore the reconstruction results. You can load results from different internal nodes or
from different gene cluster models to look for similarities or search for specific genes. You can download Rococo-Compare as a jar archive from the dowload page
or execute it using the Java WebStart technology.